Fix Windows building issue

contrib/sys/time.h

@@ -0,0 +1,38 @@
+/*
+ * MSVC compatibility shim for <sys/time.h>
+ *
+ * Provides gettimeofday() and struct timeval for Windows builds.
+ * On POSIX systems this header is never reached because the real
+ * <sys/time.h> is found first.
+ */
+
+#ifndef COMPAT_SYS_TIME_H
+#define COMPAT_SYS_TIME_H
+
+#ifdef _MSC_VER
+
+#ifndef NOMINMAX
+#define NOMINMAX  /* Prevent windows.h from defining min/max macros */
+#endif
+#include <winsock2.h>  /* struct timeval */
+#include <windows.h>
+
+static __inline int gettimeofday(struct timeval *tp, void *tzp) {
+    (void)tzp;
+    FILETIME ft;
+    unsigned __int64 tmp;
+    GetSystemTimeAsFileTime(&ft);
+    tmp = ((unsigned __int64)ft.dwHighDateTime << 32) | ft.dwLowDateTime;
+    /* FILETIME epoch is 1601-01-01; convert to Unix epoch 1970-01-01 */
+    tmp -= 116444736000000000ULL;
+    tp->tv_sec  = (long)(tmp / 10000000ULL);
+    tp->tv_usec = (long)((tmp % 10000000ULL) / 10);
+    return 0;
+}
+
+#else
+/* Non-MSVC: just include the real header */
+#include_next <sys/time.h>
+#endif
+
+#endif /* COMPAT_SYS_TIME_H */

setup.py

@@ -3,7 +3,7 @@
 #
 # Permission is hereby granted, free of charge, to any person obtaining
 # a copy of this software and associated documentation files (the
-# “Software”), to deal in the Software without restriction, including
+# "Software"), to deal in the Software without restriction, including
 # without limitation the rights to use, copy, modify, merge, publish,
 # distribute, sublicense, and/or sell copies of the Software, and to
 # permit persons to whom the Software is furnished to do so, subject to
@@ -12,7 +12,7 @@
 # The above copyright notice and this permission notice shall be included
 # in all copies or substantial portions of the Software.
 #
-# THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND,
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
 # NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
@@ -24,13 +24,27 @@
 from setuptools import setup, Extension
 import numpy
 import os
+import sys
 
 numpy_includes = [numpy.get_include()]
 
+extra_compile_args = []
+extra_link_args = []
+define_macros = []
+
+if sys.platform == 'win32':
+    # /permissive- enables C++ alternative tokens (or, and, not, etc.)
+    # /DNOMINMAX prevents windows.h from defining min/max macros
+    extra_compile_args = ['/permissive-']
+    define_macros = [('NOMINMAX', None)]
+
 lpartitionext = Extension(
             'linearpartition',
             ['linearpartitionmodule.cc'],
-            include_dirs=['LinearPartition/src', 'contrib'] + numpy_includes)
+            include_dirs=['LinearPartition/src', 'contrib'] + numpy_includes,
+            extra_compile_args=extra_compile_args,
+            extra_link_args=extra_link_args,
+            define_macros=define_macros)
 
 if not os.path.exists('LinearPartition/src/LinearPartition.cpp'):
     print('''
@@ -47,6 +61,23 @@ def patch_linearpartition_files(srcdir):
         with open(bppcpp_file, 'w') as fout:
             fout.write(content.replace('(!bpseq)', '__mea_hook__'))
 
+    # Patch LinearFoldEval.h to replace VLAs with vectors (MSVC compat)
+    evalh_file = os.path.join(srcdir, 'LinearFoldEval.h')
+    if os.path.exists(evalh_file):
+        content = open(evalh_file).read()
+        if 'long M1_energy[seq_length]' in content:
+            content = content.replace(
+                'long M1_energy[seq_length];\n    long multi_number_unpaired[seq_length];',
+                'std::vector<long> M1_energy(seq_length, 0);\n    std::vector<long> multi_number_unpaired(seq_length, 0);'
+            )
+            # Remove redundant initialization since vector constructor already zeros
+            content = content.replace(
+                'M1_energy[j] = 0; // init multi of position j\n        multi_number_unpaired[j] = 0;',
+                '// (vectors already zero-initialized)'
+            )
+            with open(evalh_file, 'w') as fout:
+                fout.write(content)
+
 patch_linearpartition_files('LinearPartition/src')
 
 setup(